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Zhang Z, Zhang L, Li J, Feng R, Li C, Liu Y, Sun G, Xiao F, Zhang C. Comprehensive analysis of m 6A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing. Comput Struct Biotechnol J 2024; 23:1144-1153. [PMID: 38510975 PMCID: PMC10950754 DOI: 10.1016/j.csbj.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
N6 adenosine methylation (m6A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6A regulators on acute myeloid leukemia (AML). However, the global m6A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing. Notably, the amount of m6A sites and the m6A levels in CR BMs was significantly lower than those in the AML BMs. Such a significant reduction in the m6A levels was also detected in AZA-treated HL-60 cells. Thirteen genes with decreased m6A and expression levels were identified, among which three genes (HPRT1, SNRPC, and ANP32B) were closely related to the prognosis of AML. Finally, we speculated the mechanism via which m6A modifications affected the mRNA stability of these three genes. In conclusion, we illustrated for the first time the global landscape of m6A levels in AZA plus VEN treated AML (CR) patients and revealed that AZA had a significant demethylation effect at the RNA level in AML patients. In addition, we identified new biomarkers for AZA plus VEN-treated AML via Nanopore sequencing technology in RNA epigenetics.
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Affiliation(s)
- Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing 100730, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lili Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiangtao Li
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ru Feng
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chang Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology of National Health Commission, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, 9 DongDan Santiao, Beijing 100730, China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunli Zhang
- Department of Hematology, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024; 23:3235-3248. [PMID: 38412263 PMCID: PMC11301670 DOI: 10.1021/acs.jproteome.3c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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3
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Mochmann LH, Treue D, Bockmayr M, Silva P, Zasada C, Mastrobuoni G, Bayram S, Forbes M, Jurmeister P, Liebig S, Blau O, Schleich K, Splettstoesser B, Nordmann TM, von der Heide EK, Isaakidis K, Schulze V, Busch C, Siddiq H, Schlee C, Hester S, Fransecky L, Neumann M, Kempa S, Klauschen F, Baldus CD. Proteomic profiling reveals ACSS2 facilitating metabolic support in acute myeloid leukemia. Cancer Gene Ther 2024:10.1038/s41417-024-00785-5. [PMID: 38851813 DOI: 10.1038/s41417-024-00785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/19/2024] [Accepted: 05/16/2024] [Indexed: 06/10/2024]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by genomic aberrations in oncogenes, cytogenetic abnormalities, and an aberrant epigenetic landscape. Nearly 50% of AML cases will relapse with current treatment. A major source of therapy resistance is the interaction of mesenchymal stroma with leukemic cells resulting in therapeutic protection. We aimed to determine pro-survival/anti-apoptotic protein networks involved in the stroma protection of leukemic cells. Proteomic profiling of cultured primary AML (n = 14) with Hs5 stroma cell line uncovered an up-regulation of energy-favorable metabolic proteins. Next, we modulated stroma-induced drug resistance with an epigenetic drug library, resulting in reduced apoptosis with histone deacetylase inhibitor (HDACi) treatment versus other epigenetic modifying compounds. Quantitative phosphoproteomic probing of this effect further revealed a metabolic-enriched phosphoproteome including significant up-regulation of acetyl-coenzyme A synthetase (ACSS2, S30) in leukemia-stroma HDACi treated cocultures compared with untreated monocultures. Validating these findings, we show ACSS2 substrate, acetate, promotes leukemic proliferation, ACSS2 knockout in leukemia cells inhibits leukemic proliferation and ACSS2 knockout in the stroma impairs leukemic metabolic fitness. Finally, we identify ACSS1/ACSS2-high expression AML subtype correlating with poor overall survival. Collectively, this study uncovers the leukemia-stroma phosphoproteome emphasizing a role for ACSS2 in mediating AML growth and drug resistance.
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Affiliation(s)
- Liliana H Mochmann
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Denise Treue
- Institute of Pathology Berlin, Charité - Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Berlin, Germany
| | - Michael Bockmayr
- Institute of Pathology Berlin, Charité - Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Berlin, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Patricia Silva
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Christin Zasada
- Berlin Institute for Medical Systems Biology (BIMSB) at Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology (BIMSB) at Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Safak Bayram
- Berlin Institute for Medical Systems Biology (BIMSB) at Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Martin Forbes
- Berlin Institute for Medical Systems Biology (BIMSB) at Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Philipp Jurmeister
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Liebig
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Olga Blau
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Konstanze Schleich
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Thierry M Nordmann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Eva K von der Heide
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Konstandina Isaakidis
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Veronika Schulze
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Caroline Busch
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Hafsa Siddiq
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Cornelia Schlee
- Department of Hematology and Oncology, Charité - Universitätsmedizin Berlin, a Corporate Member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Campus Benjamin Franklin, Berlin, Germany
| | - Svenja Hester
- Department of Biochemistry, Oxford University, Oxford, UK
| | - Lars Fransecky
- Department of Hematology and Oncology, UKSH, Campus Kiel, Kiel, Germany
| | - Martin Neumann
- Department of Hematology and Oncology, UKSH, Campus Kiel, Kiel, Germany
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology (BIMSB) at Max Delbruck Center for Molecular Medicine, Berlin, Germany.
| | - Frederick Klauschen
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany.
- Institute of Pathology Berlin, Charité - Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin, Humboldt-Universität, and Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Claudia D Baldus
- Department of Hematology and Oncology, UKSH, Campus Kiel, Kiel, Germany.
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Kim DY, Shin DY, Oh S, Kim I, Kim EJ. Gene Expression and DNA Methylation Profiling Suggest Potential Biomarkers for Azacitidine Resistance in Myelodysplastic Syndrome. Int J Mol Sci 2024; 25:4723. [PMID: 38731939 PMCID: PMC11083267 DOI: 10.3390/ijms25094723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Myelodysplastic syndrome/neoplasm (MDS) comprises a group of heterogeneous hematopoietic disorders that present with genetic mutations and/or cytogenetic changes and, in the advanced stage, exhibit wide-ranging gene hypermethylation. Patients with higher-risk MDS are typically treated with repeated cycles of hypomethylating agents, such as azacitidine. However, some patients fail to respond to this therapy, and fewer than 50% show hematologic improvement. In this context, we focused on the potential use of epigenetic data in clinical management to aid in diagnostic and therapeutic decision-making. First, we used the F-36P MDS cell line to establish an azacitidine-resistant F-36P cell line. We performed expression profiling of azacitidine-resistant and parental F-36P cells and used biological and bioinformatics approaches to analyze candidate azacitidine-resistance-related genes and pathways. Eighty candidate genes were identified and found to encode proteins previously linked to cancer, chronic myeloid leukemia, and transcriptional misregulation in cancer. Interestingly, 24 of the candidate genes had promoter methylation patterns that were inversely correlated with azacitidine resistance, suggesting that DNA methylation status may contribute to azacitidine resistance. In particular, the DNA methylation status and/or mRNA expression levels of the four genes (AMER1, HSPA2, NCX1, and TNFRSF10C) may contribute to the clinical effects of azacitidine in MDS. Our study provides information on azacitidine resistance diagnostic genes in MDS patients, which can be of great help in monitoring the effectiveness of treatment in progressing azacitidine treatment for newly diagnosed MDS patients.
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Affiliation(s)
- Da Yeon Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea;
- Department of Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Dong-Yeop Shin
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (D.-Y.S.); (S.O.)
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Somi Oh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (D.-Y.S.); (S.O.)
| | - Inho Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; (D.-Y.S.); (S.O.)
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Eun Ju Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul 01812, Republic of Korea;
- Department of Radiological and Medico-Oncological Sciences, University of Science and Technology, Daejeon 34113, Republic of Korea
- Institute for Molecular Bioscience, The University of Queensland, Carmody Rd., St Lucia, Brisbane, QLD 4072, Australia
- Genomics and Machine Learning Lab, QIMR Berghofer Medical Research Institute, Herston Rd., Herston, Brisbane, QLD 4006, Australia
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5
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Tanaka T, Kudo K, Kanezaki R, Yuzawa K, Toki T, Okuse R, Kobayashi A, Sato T, Kamio T, Terui K, Ito E. Antileukemic effect of azacitidine, a DNA methyltransferase inhibitor, on cell lines of myeloid leukemia associated with Down syndrome. Exp Hematol 2024; 132:104179. [PMID: 38342295 DOI: 10.1016/j.exphem.2024.104179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 01/12/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Myeloid leukemia associated with Down syndrome (ML-DS) responds well to chemotherapy and has a favorable prognosis, but the clinical outcome of patients with refractory or relapsed ML-DS is dismal. We recently reported a case of relapsed ML-DS with an effective response to a DNA methyltransferase inhibitor, azacitidine (AZA). However, the efficacy of AZA for refractory or relapsed ML-DS remains uncertain. Here, we investigated the effects and mechanism of action of AZA on three ML-DS cell lines derived from relapsed cases. AZA inhibited the proliferation of all examined ML-DS cell lines to the same extent as that of AZA-sensitive acute myeloid leukemia non-Down syndrome cell lines. Transient low-dose AZA treatment exerted durable antileukemic effects on ML-DS cells. The inhibitory effect included cell cycle arrest, apoptosis, and reduction of aldehyde dehydrogenase activity. Comprehensive differential gene expression analysis showed that AZA induced megakaryocytic differentiation in all ML-DS cell lines examined. Furthermore, AZA induced activation of type I interferon-stimulated genes, primarily involved in antiproliferation signaling, without stimulation of the interferon receptor-mediated autocrine system. Activation of the type I interferon pathway by stimulation with interferon-α exerted antiproliferative effects on ML-DS cells, suggesting that AZA exerts its antileukemic effects on ML-DS cells at least partially through the type I interferon pathway. Moreover, the effect of AZA on normal hematopoiesis did not differ significantly between individuals with non-Down syndrome and Down syndrome. In summary, this study suggests that AZA is a potentially effective treatment option for ML-DS disease control, including relapsed cases, and has reduced side effects.
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Affiliation(s)
- Tatsuhiko Tanaka
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ko Kudo
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Rika Kanezaki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kentaro Yuzawa
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ryo Okuse
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Akie Kobayashi
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tomohiko Sato
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Takuya Kamio
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan; Department of Community Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.
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Jeyaraju DV, Alapa M, Polonskaia A, Risueño A, Subramanyam P, Anand A, Ghosh K, Kyriakopoulos C, Hemerich D, Hurren R, Wang X, Gronda M, Ahsan A, Chiu H, Thomas G, Lind EF, Menezes DL, Schimmer AD, Hagner PR, Gandhi A, Thakurta AG. Extended exposure to low doses of azacitidine induces differentiation of leukemic stem cells through activation of myeloperoxidase. Haematologica 2024; 109:1082-1094. [PMID: 37941406 PMCID: PMC10985425 DOI: 10.3324/haematol.2023.283437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Oral azacitidine (oral-Aza) treatment results in longer median overall survival (OS) (24.7 vs. 14.8 months in placebo) in patients with acute myeloid leukemia (AML) in remission after intensive chemotherapy. The dosing schedule of oral-Aza (14 days/28-day cycle) allows for low exposure of Aza for an extended duration thereby facilitating a sustained therapeutic effect. However, the underlying mechanisms supporting the clinical impact of oral-Aza in maintenance therapy remain to be fully understood. In this preclinical work, we explore the mechanistic basis of oral-Aza/extended exposure to Aza through in vitro and in vivo modeling. In cell lines, extended exposure to Aza results in sustained DNMT1 loss, leading to durable hypomethylation, and gene expression changes. In mouse models, extended exposure to Aza, preferentially targets immature leukemic cells. In leukemic stem cell (LSC) models, the extended dose of Aza induces differentiation and depletes CD34+CD38- LSC. Mechanistically, LSC differentiation is driven in part by increased myeloperoxidase (MPO) expression. Inhibition of MPO activity either by using an MPO-specific inhibitor or blocking oxidative stress, a known mechanism of MPO, partly reverses the differentiation of LSC. Overall, our preclinical work reveals novel mechanistic insights into oral-Aza and its ability to target LSC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Rose Hurren
- Princess Margaret Cancer Centre, Toronto, ON
| | | | | | | | | | | | - Evan F Lind
- Department of Molecular Microbiology and the Knight Cancer Institute, Oregon Health and Science University, Portland, OR
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7
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Humphries S, Bond DR, Germon ZP, Keely S, Enjeti AK, Dun MD, Lee HJ. Crosstalk between DNA methylation and hypoxia in acute myeloid leukaemia. Clin Epigenetics 2023; 15:150. [PMID: 37705055 PMCID: PMC10500762 DOI: 10.1186/s13148-023-01566-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a deadly disease characterised by the uncontrolled proliferation of immature myeloid cells within the bone marrow. Altered regulation of DNA methylation is an important epigenetic driver of AML, where the hypoxic bone marrow microenvironment can help facilitate leukaemogenesis. Thus, interactions between epigenetic regulation and hypoxia signalling will have important implications for AML development and treatment. MAIN BODY This review summarises the importance of DNA methylation and the hypoxic bone marrow microenvironment in the development, progression, and treatment of AML. Here, we focus on the role hypoxia plays on signalling and the subsequent regulation of DNA methylation. Hypoxia is likely to influence DNA methylation through altered metabolic pathways, transcriptional control of epigenetic regulators, and direct effects on the enzymatic activity of epigenetic modifiers. DNA methylation may also prevent activation of hypoxia-responsive genes, demonstrating bidirectional crosstalk between epigenetic regulation and the hypoxic microenvironment. Finally, we consider the clinical implications of these interactions, suggesting that reduced cell cycling within the hypoxic bone marrow may decrease the efficacy of hypomethylating agents. CONCLUSION Hypoxia is likely to influence AML progression through complex interactions with DNA methylation, where the therapeutic efficacy of hypomethylating agents may be limited within the hypoxic bone marrow. To achieve optimal outcomes for AML patients, future studies should therefore consider co-treatments that can promote cycling of AML cells within the bone marrow or encourage their dissociation from the bone marrow.
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Affiliation(s)
- Sam Humphries
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Danielle R Bond
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Zacary P Germon
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Anoop K Enjeti
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Department of Haematology, Calvary Mater Hospital, Waratah, NSW, 2298, Australia
- New South Wales Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Heather J Lee
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
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8
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Liang G, Wang L, You Q, Cahill K, Chen C, Zhang W, Fulton N, Stock W, Odenike O, He C, Han D. Cellular Composition and 5hmC Signature Predict the Treatment Response of AML Patients to Azacitidine Combined with Chemotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300445. [PMID: 37271891 PMCID: PMC10427370 DOI: 10.1002/advs.202300445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/12/2023] [Indexed: 06/06/2023]
Abstract
Azacitidine (AZA) is a DNA methyltransferase inhibitor and epigenetic modulator that can be an effective agent in combination with chemotherapy for patients with high-risk acute myeloid leukemia (AML). However, biological factors driving the therapeutic response of such hypomethylating agent (HMA)-based therapies remain unknown. Herein, the transcriptome and/or genome-wide 5-hydroxymethylcytosine (5hmC) is characterized for 41 patients with high-risk AML from a phase 1 clinical trial treated with AZA epigenetic priming followed by high-dose cytarabine and mitoxantrone (AZA-HiDAC-Mito). Digital cytometry reveals that responders have elevated Granulocyte-macrophage-progenitor-like (GMP-like) malignant cells displaying an active cell cycle program. Moreover, the enrichment of natural killer (NK) cells predicts a favorable outcome in patients receiving AZA-HiDAC-Mito therapy or other AZA-based therapies. Comparing 5hmC profiles before and after five-day treatment of AZA shows that AZA exposure induces dose-dependent 5hmC changes, in which the magnitude correlates with overall survival (p = 0.015). An extreme gradient boosting (XGBoost) machine learning model is developed to predict the treatment response based on 5hmC levels of 11 genes, achieving an area under the curve (AUC) of 0.860. These results suggest that cellular composition markedly impacts the treatment response, and showcase the prospect of 5hmC signatures in predicting the outcomes of HMA-based therapies in AML.
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Affiliation(s)
- Guanghao Liang
- Key Laboratory of Genomic and Precision MedicineBeijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- College of Future TechnologySino‐Danish CollegeUniversity of Chinese Academy of SciencesBeijing100049China
| | - Linchen Wang
- Key Laboratory of Genomic and Precision MedicineBeijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- College of Future TechnologySino‐Danish CollegeUniversity of Chinese Academy of SciencesBeijing100049China
| | - Qiancheng You
- Department of Chemistry and Institute for Biophysical DynamicsThe University of ChicagoChicagoIL60637USA
- Howard Hughes Medical InstituteChicagoIL60637USA
| | - Kirk Cahill
- Section of Hematology/OncologyDepartment of MedicineUniversity of Chicago MedicineChicagoIL60637USA
| | - Chuanyuan Chen
- Key Laboratory of Genomic and Precision MedicineBeijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- College of Future TechnologySino‐Danish CollegeUniversity of Chinese Academy of SciencesBeijing100049China
| | - Wei Zhang
- Department of MedicineUniversity of California, San DiegoLa JollaCA92093USA
- Bristol‐Myers SquibbSan DiegoCA92121USA
| | - Noreen Fulton
- Section of Hematology/OncologyDepartment of MedicineUniversity of Chicago MedicineChicagoIL60637USA
- Comprehensive Cancer CenterUniversity of Chicago MedicineChicagoIL60637USA
| | - Wendy Stock
- Section of Hematology/OncologyDepartment of MedicineUniversity of Chicago MedicineChicagoIL60637USA
- Comprehensive Cancer CenterUniversity of Chicago MedicineChicagoIL60637USA
| | - Olatoyosi Odenike
- Section of Hematology/OncologyDepartment of MedicineUniversity of Chicago MedicineChicagoIL60637USA
- Comprehensive Cancer CenterUniversity of Chicago MedicineChicagoIL60637USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical DynamicsThe University of ChicagoChicagoIL60637USA
- Howard Hughes Medical InstituteChicagoIL60637USA
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIL60637USA
| | - Dali Han
- Key Laboratory of Genomic and Precision MedicineBeijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- College of Future TechnologySino‐Danish CollegeUniversity of Chinese Academy of SciencesBeijing100049China
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijing100101China
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9
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Karantanos T, Teodorescu P, Arvanitis M, Perkins B, Jain T, DeZern AE, Dalton WB, Christodoulou I, Paun BC, Varadhan R, Esteb C, Rajkhowa T, Bonifant C, Gondek LP, Levis MJ, Yegnasubramanian S, Ghiaur G, Jones RJ. CCRL2 affects the sensitivity of myelodysplastic syndrome and secondary acute myeloid leukemia cells to azacitidine. Haematologica 2023; 108:1886-1899. [PMID: 36519323 PMCID: PMC10316237 DOI: 10.3324/haematol.2022.281444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Better understanding of the biology of resistance to DNA methyltransferase (DNMT) inhibitors is required to identify therapies that can improve their efficacy for patients with high-risk myelodysplastic syndrome (MDS). CCRL2 is an atypical chemokine receptor that is upregulated in CD34+ cells from MDS patients and induces proliferation of MDS and secondary acute myeloid leukemia (sAML) cells. In this study, we evaluated any role that CCRL2 may have in the regulation of pathways associated with poor response or resistance to DNMT inhibitors. We found that CCRL2 knockdown in TF-1 cells downregulated DNA methylation and PRC2 activity pathways and increased DNMT suppression by azacitidine in MDS/sAML cell lines (MDS92, MDS-L and TF-1). Consistently, CCRL2 deletion increased the sensitivity of these cells to azacitidine in vitro and the efficacy of azacitidine in an MDS-L xenograft model. Furthermore, CCRL2 overexpression in MDS-L and TF-1 cells decreased their sensitivity to azacitidine. Finally, CCRL2 levels were higher in CD34+ cells from MDS and MDS/myeloproliferative neoplasm patients with poor response to DNMT inhibitors. In conclusion, we demonstrated that CCRL2 modulates epigenetic regulatory pathways, particularly DNMT levels, and affects the sensitivity of MDS/sAML cells to azacitidine. These results support CCRL2 targeting as having therapeutic potential in MDS/sAML.
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Affiliation(s)
- Theodoros Karantanos
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore.
| | - Patric Teodorescu
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Marios Arvanitis
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore
| | - Brandy Perkins
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Tania Jain
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Amy E DeZern
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - W Brian Dalton
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Ilias Christodoulou
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Bogdan C Paun
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Ravi Varadhan
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Christopher Esteb
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Trivikram Rajkhowa
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Challice Bonifant
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Mark J Levis
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Srinivasan Yegnasubramanian
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Gabriel Ghiaur
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Richard J Jones
- Division of Hematological Malignancies, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
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10
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Liu J, Min S, Kim D, Park J, Park E, Koh Y, Shin DY, Kim TK, Byun JM, Yoon SS, Hong J. Epigenetic priming improves salvage chemotherapy in diffuse large B-cell lymphoma via endogenous retrovirus-induced cGAS-STING activation. Clin Epigenetics 2023; 15:75. [PMID: 37138342 PMCID: PMC10155448 DOI: 10.1186/s13148-023-01493-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Although most patients with diffuse large B-cell lymphoma (DLBCL) achieve complete remission after first-line rituximab-containing immunochemotherapy, up to 40% of patients relapse and require salvage therapy. Among those patients, a substantial proportion remain refractory to salvage therapy due to insufficient efficacy or intolerance of toxicities. A hypomethylating agent, 5-azacytidine, showed a chemosensitizing effect when primed before chemotherapy in lymphoma cell lines and newly diagnosed DLBCL patients. However, its potential to improve outcomes of salvage chemotherapy in DLBCL has not been investigated. RESULTS In this study, we demonstrated the mechanism of 5-azacytidine priming as a chemosensitizer in a platinum-based salvage regimen. This chemosensitizing effect was associated with endogenous retrovirus (ERV)-induced viral mimicry responses via the cGAS-STING axis. We found deficiency of cGAS impaired the chemosensitizing effect of 5-azacytidine. Furthermore, combining vitamin C and 5-azacytidine to synergistically activate STING could be a potential remedy for insufficient priming induced by 5-azacytidine alone. CONCLUSIONS Taken together, the chemosensitizing effect of 5-azacytidine could be exploited to overcome the limitations of the current platinum-containing salvage chemotherapy in DLBCL and the status of cGAS-STING has the potential to predict the efficacy of 5-azacytidine priming.
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Affiliation(s)
- Jun Liu
- College of Medicine, Zhejiang University, Hangzhou, China
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suji Min
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongchan Kim
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunchae Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngil Koh
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ja Min Byun
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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11
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Skopek R, Palusińska M, Kaczor-Keller K, Pingwara R, Papierniak-Wyglądała A, Schenk T, Lewicki S, Zelent A, Szymański Ł. Choosing the Right Cell Line for Acute Myeloid Leukemia (AML) Research. Int J Mol Sci 2023; 24:5377. [PMID: 36982453 PMCID: PMC10049680 DOI: 10.3390/ijms24065377] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Immortalized cell lines are widely used in vitro tools in oncology and hematology research. While these cell lines represent artificial systems and may accumulate genetic aberrations with each passage, they are still considered valuable models for pilot, preliminary, and screening studies. Despite their limitations, cell lines are cost-effective and provide repeatable and comparable results. Choosing the appropriate cell line for acute myeloid leukemia (AML) research is crucial for obtaining reliable and relevant results. Several factors should be considered when selecting a cell line for AML research, such as specific markers and genetic abnormalities associated with different subtypes of AML. It is also essential to evaluate the karyotype and mutational profile of the cell line, as these can influence the behavior and response to the treatment of the cells. In this review, we evaluate immortalized AML cell lines and discuss the issues surrounding them concerning the revised World Health Organization and the French-American-British classifications.
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Affiliation(s)
- Rafał Skopek
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Małgorzata Palusińska
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Katarzyna Kaczor-Keller
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Rafał Pingwara
- Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-787 Warsaw, Poland
| | | | - Tino Schenk
- Department of Hematology and Medical Oncology, Clinic of Internal Medicine II, Jena University Hospital, 07747 Jena, Germany
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, 07747 Jena, Germany
| | - Sławomir Lewicki
- Faculty of Medical Sciences and Health Sciences, Kazimierz Pulaski University of Technology and Humanities, 26-600 Radom, Poland
- Institute of Outcomes Research, Maria Sklodowska-Curie Medical Academy, 00-001 Warsaw, Poland
| | - Artur Zelent
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Łukasz Szymański
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
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12
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Zavras PD, Sinanidis I, Tsakiroglou P, Karantanos T. Understanding the Continuum between High-Risk Myelodysplastic Syndrome and Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24055018. [PMID: 36902450 PMCID: PMC10002503 DOI: 10.3390/ijms24055018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Myelodysplastic syndrome (MDS) is a clonal hematopoietic neoplasm characterized by bone marrow dysplasia, failure of hematopoiesis and variable risk of progression to acute myeloid leukemia (AML). Recent large-scale studies have demonstrated that distinct molecular abnormalities detected at earlier stages of MDS alter disease biology and predict progression to AML. Consistently, various studies analyzing these diseases at the single-cell level have identified specific patterns of progression strongly associated with genomic alterations. These pre-clinical results have solidified the conclusion that high-risk MDS and AML arising from MDS or AML with MDS-related changes (AML-MRC) represent a continuum of the same disease. AML-MRC is distinguished from de novo AML by the presence of certain chromosomal abnormalities, such as deletion of 5q, 7/7q, 20q and complex karyotype and somatic mutations, which are also present in MDS and carry crucial prognostic implications. Recent changes in the classification and prognostication of MDS and AML by the International Consensus Classification (ICC) and the World Health Organization (WHO) reflect these advances. Finally, a better understanding of the biology of high-risk MDS and the mechanisms of disease progression have led to the introduction of novel therapeutic approaches, such as the addition of venetoclax to hypomethylating agents and, more recently, triplet therapies and agents targeting specific mutations, including FLT3 and IDH1/2. In this review, we analyze the pre-clinical data supporting that high-risk MDS and AML-MRC share the same genetic abnormalities and represent a continuum, describe the recent changes in the classification of these neoplasms and summarize the advances in the management of patients with these neoplasms.
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13
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Ciaglia T, Vestuto V, Bertamino A, González-Muñiz R, Gómez-Monterrey I. On the modulation of TRPM channels: Current perspectives and anticancer therapeutic implications. Front Oncol 2023; 12:1065935. [PMID: 36844925 PMCID: PMC9948629 DOI: 10.3389/fonc.2022.1065935] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023] Open
Abstract
The transient melastatin receptor potential (TRPM) ion channel subfamily functions as cellular sensors and transducers of critical biological signal pathways by regulating ion homeostasis. Some members of TRPM have been cloned from cancerous tissues, and their abnormal expressions in various solid malignancies have been correlated with cancer cell growth, survival, or death. Recent evidence also highlights the mechanisms underlying the role of TRPMs in tumor epithelial-mesenchymal transition (EMT), autophagy, and cancer metabolic reprogramming. These implications support TRPM channels as potential molecular targets and their modulation as an innovative therapeutic approach against cancer. Here, we discuss the general characteristics of the different TRPMs, focusing on current knowledge about the connection between TRPM channels and critical features of cancer. We also cover TRPM modulators used as pharmaceutical tools in biological trials and an indication of the only clinical trial with a TRPM modulator about cancer. To conclude, the authors describe the prospects for TRPM channels in oncology.
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Affiliation(s)
- Tania Ciaglia
- Dipartimento di Farmacia (DIFARMA), Università degli Studi di Salerno, Fisciano, Italy
| | - Vincenzo Vestuto
- Dipartimento di Farmacia (DIFARMA), Università degli Studi di Salerno, Fisciano, Italy
| | - Alessia Bertamino
- Dipartimento di Farmacia (DIFARMA), Università degli Studi di Salerno, Fisciano, Italy
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14
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Pance K, Gramespacher JA, Byrnes JR, Salangsang F, Serrano JAC, Cotton AD, Steri V, Wells JA. Modular cytokine receptor-targeting chimeras for targeted degradation of cell surface and extracellular proteins. Nat Biotechnol 2023; 41:273-281. [PMID: 36138170 PMCID: PMC9931583 DOI: 10.1038/s41587-022-01456-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 12/20/2022]
Abstract
Targeted degradation of cell surface and extracellular proteins via lysosomal delivery is an important means to modulate extracellular biology. However, these approaches have limitations due to lack of modularity, ease of development, restricted tissue targeting and applicability to both cell surface and extracellular proteins. We describe a lysosomal degradation strategy, termed cytokine receptor-targeting chimeras (KineTACs), that addresses these limitations. KineTACs are fully genetically encoded bispecific antibodies consisting of a cytokine arm, which binds its cognate cytokine receptor, and a target-binding arm for the protein of interest. We show that KineTACs containing the cytokine CXCL12 can use the decoy recycling receptor, CXCR7, to target a variety of target proteins to the lysosome for degradation. Additional KineTACs were designed to harness other CXCR7-targeting cytokines, CXCL11 and vMIPII, and the interleukin-2 (IL-2) receptor-targeting cytokine IL-2. Thus, KineTACs represent a general, modular, selective and simple genetically encoded strategy for inducing lysosomal delivery of extracellular and cell surface targets with broad or tissue-specific distribution.
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Affiliation(s)
- Katarina Pance
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,EpiBiologics, Inc., San Carlos, CA, USA
| | - Josef A Gramespacher
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,EpiBiologics, Inc., San Carlos, CA, USA
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - Juan-Antonio C Serrano
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - Adam D Cotton
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Preclinical Therapeutics Core, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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15
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Cheung LC, Aya-Bonilla C, Cruickshank MN, Chiu SK, Kuek V, Anderson D, Chua GA, Singh S, Oommen J, Ferrari E, Hughes AM, Ford J, Kunold E, Hesselman MC, Post F, Faulk KE, Breese EH, Guest EM, Brown PA, Loh ML, Lock RB, Kees UR, Jafari R, Malinge S, Kotecha RS. Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged acute lymphoblastic leukemia reveals a new therapeutic strategy. Leukemia 2023; 37:61-71. [PMID: 36380143 PMCID: PMC9883157 DOI: 10.1038/s41375-022-01746-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
Infants with KMT2A-rearranged B-cell acute lymphoblastic leukemia (ALL) have a dismal prognosis. Survival outcomes have remained static in recent decades despite treatment intensification and novel therapies are urgently required. KMT2A-rearranged infant ALL cells are characterized by an abundance of promoter hypermethylation and exhibit high BCL-2 expression, highlighting potential for therapeutic targeting. Here, we show that hypomethylating agents exhibit in vitro additivity when combined with most conventional chemotherapeutic agents. However, in a subset of samples an antagonistic effect was seen between several agents. This was most evident when hypomethylating agents were combined with methotrexate, with upregulation of ATP-binding cassette transporters identified as a potential mechanism. Single agent treatment with azacitidine and decitabine significantly prolonged in vivo survival in KMT2A-rearranged infant ALL xenografts. Treatment of KMT2A-rearranged infant ALL cell lines with azacitidine and decitabine led to differential genome-wide DNA methylation, changes in gene expression and thermal proteome profiling revealed the target protein-binding landscape of these agents. The selective BCL-2 inhibitor, venetoclax, exhibited in vitro additivity in combination with hypomethylating or conventional chemotherapeutic agents. The addition of venetoclax to azacitidine resulted in a significant in vivo survival advantage indicating the therapeutic potential of this combination to improve outcome for infants with KMT2A-rearranged ALL.
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Affiliation(s)
- Laurence C Cheung
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Carlos Aya-Bonilla
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | | | - Sung K Chiu
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Vincent Kuek
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- Curtin Medical School, Curtin University, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Grace-Alyssa Chua
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Sajla Singh
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Joyce Oommen
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Emanuela Ferrari
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Anastasia M Hughes
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Jette Ford
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Elena Kunold
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Maria C Hesselman
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Frederik Post
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Kelly E Faulk
- University of Colorado Anschutz Medical Campus, Children's Hospital Colorado, Aurora, CO, USA
| | - Erin H Breese
- Cancer and Blood Diseases Institute, Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin M Guest
- Division of Hematology, Oncology, Blood and Marrow Transplantation, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center, John Hopkins University, Baltimore, MD, USA
| | - Mignon L Loh
- Division of Pediatric Hematology, Oncology, Bone Marrow Transplant and Cellular Therapy, Seattle Children's Hospital, Seattle, WA, USA
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre/School of Women's and Children's Health/UNSW Centre for Childhood Cancer Research, UNSW Sydney, Kensington, NSW, Australia
| | - Ursula R Kees
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rozbeh Jafari
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Sébastien Malinge
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia
- The University of Western Australia, Perth, WA, Australia
| | - Rishi S Kotecha
- Leukaemia Translational Research Laboratory, Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA, Australia.
- Curtin Medical School, Curtin University, Perth, WA, Australia.
- The University of Western Australia, Perth, WA, Australia.
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children's Hospital, Perth, WA, Australia.
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16
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A Bioinformatics View on Acute Myeloid Leukemia Surface Molecules by Combined Bayesian and ABC Analysis. Bioengineering (Basel) 2022; 9:bioengineering9110642. [DOI: 10.3390/bioengineering9110642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
“Big omics data” provoke the challenge of extracting meaningful information with clinical benefit. Here, we propose a two-step approach, an initial unsupervised inspection of the structure of the high dimensional data followed by supervised analysis of gene expression levels, to reconstruct the surface patterns on different subtypes of acute myeloid leukemia (AML). First, Bayesian methodology was used, focusing on surface molecules encoded by cluster of differentiation (CD) genes to assess whether AML is a homogeneous group or segregates into clusters. Gene expressions of 390 patient samples measured using microarray technology and 150 samples measured via RNA-Seq were compared. Beyond acute promyelocytic leukemia (APL), a well-known AML subentity, the remaining AML samples were separated into two distinct subgroups. Next, we investigated which CD molecules would best distinguish each AML subgroup against APL, and validated discriminative molecules of both datasets by searching the scientific literature. Surprisingly, a comparison of both omics analyses revealed that CD339 was the only overlapping gene differentially regulated in APL and other AML subtypes. In summary, our two-step approach for gene expression analysis revealed two previously unknown subgroup distinctions in AML based on surface molecule expression, which may guide the differentiation of subentities in a given clinical–diagnostic context.
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17
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Karantanos T, Tsai HL, Gondek LP, DeZern AE, Ghiaur G, Dalton WB, Gojo I, Prince GT, Webster J, Ambinder A, Smith BD, Levis MJ, Varadhan R, Jones RJ, Jain T. Genomic landscape of myelodysplastic/myeloproliferative neoplasm can predict response to hypomethylating agent therapy. Leuk Lymphoma 2022; 63:1942-1948. [PMID: 35379077 PMCID: PMC9847567 DOI: 10.1080/10428194.2022.2057488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There are currently no known predictors of myelodysplastic syndrome (MDS)/myeloproliferative overlap neoplasm (MPN) patients' response to hypomethylating agents (HMA). Forty-three patients with MDS/MPN who were treated with HMA during chronic phase and had next-generation sequencing using the established 63-genes panel were identified. Complete and partial remission and marrow response were assessed based on the MDS/MPN International Working Group response criteria. On univariate analysis, younger age, higher number of mutations, and mutations in SETBP1, RUNX1, or EZH2 were associated with no response. Multivariable analysis for modeling response were conducted via least absolute shrinkage and selection operator logistic regression approach, and showed that mutations in SETBP1, RUNX1, or EZH2 predict lack of HMA response. While limited by sample size, our findings suggest that genomic landscape can potentially identify MDS/MPN patients with lower likelihood of response to HMA.
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Affiliation(s)
- Theodoras Karantanos
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hua-Ling Tsai
- Division of Biostatistics and Bioinformatics, Johns Hopkins/Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Lukasz P. Gondek
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Amy E. DeZern
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriel Ghiaur
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - W. Brian Dalton
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ivana Gojo
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Gabrielis T. Prince
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan Webster
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Alexander Ambinder
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - B. Douglas Smith
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Mark J Levis
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ravi Varadhan
- Division of Biostatistics and Bioinformatics, Johns Hopkins/Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Richard J. Jones
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Tania Jain
- Division of Hematological Malignancies and Bone Marrow Transplantation, Sidney Kimrnel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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18
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Upadhyay P, Beales J, Shah NM, Gruszczynska A, Miller CA, Petti AA, Ramakrishnan SM, Link DC, Ley TJ, Welch JS. Recurrent transcriptional responses in AML and MDS patients treated with decitabine. Exp Hematol 2022; 111:50-65. [PMID: 35429619 PMCID: PMC9833843 DOI: 10.1016/j.exphem.2022.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 01/21/2023]
Abstract
The molecular events responsible for decitabine responses in myelodysplastic syndrome and acute myeloid leukemia patients are poorly understood. Decitabine has a short serum half-life and limited stability in tissue culture. Therefore, theoretical pharmacologic differences may exist between patient molecular changes in vitro and the consequences of in vivo treatment. To systematically identify the global genomic and transcriptomic alterations induced by decitabine in vivo, we evaluated primary bone marrow samples that were collected during patient treatment and applied whole-genome bisulfite sequencing, RNA-sequencing, and single-cell RNA sequencing. Decitabine induced global, reversible hypomethylation after 10 days of therapy in all patients, which was associated with induction of interferon-induced pathways, the expression of endogenous retroviral elements, and inhibition of erythroid-related transcripts, recapitulating many effects seen previously in in vitro studies. However, at relapse after decitabine treatment, interferon-induced transcripts remained elevated relative to day 0, but erythroid-related transcripts now were more highly expressed than at day 0. Clinical responses were not correlated with epigenetic or transcriptional signatures, although sample size and interpatient variance restricted the statistical power required for capturing smaller effects. Collectively, these data define global hypomethylation by decitabine and find that erythroid-related pathways may be relevant because they are inhibited by therapy and reverse at relapse.
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Affiliation(s)
- Pawan Upadhyay
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jeremy Beales
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Nakul M. Shah
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Agata Gruszczynska
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Allegra A. Petti
- Department of Neuro-logical Surgery, Washington University School of Medicine, St. Louis, MO
| | - Sai Mukund Ramakrishnan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy J. Ley
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - John S. Welch
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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19
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Ali SS, Raj R, Kaur T, Weadick B, Nayak D, No M, Protos J, Odom H, Desai K, Persaud AK, Wang J, Govindarajan R. Solute Carrier Nucleoside Transporters in Hematopoiesis and Hematological Drug Toxicities: A Perspective. Cancers (Basel) 2022; 14:cancers14133113. [PMID: 35804885 PMCID: PMC9264962 DOI: 10.3390/cancers14133113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Anticancer nucleoside analogs are promising treatments that often result in damaging toxicities and therefore ineffective treatment. Mechanisms of this are not well-researched, but cellular nucleoside transport research in mice might provide additional insight given transport’s role in mammalian hematopoiesis. Cellular nucleoside transport is a notable component of mammalian hematopoiesis due to how mutations within it relate to hematological abnormities. This review encompasses nucleoside transporters, focusing on their inherent properties, hematopoietic role, and their interplay in nucleoside drug treatment side effects. We then propose potential mechanisms to explain nucleoside transport involvement in blood disorders. Finally, we point out and advocate for future research areas that would improve therapeutic outcomes for patients taking nucleoside analog therapies. Abstract Anticancer nucleoside analogs produce adverse, and at times, dose-limiting hematological toxicities that can compromise treatment efficacy, yet the mechanisms of such toxicities are poorly understood. Recently, cellular nucleoside transport has been implicated in normal blood cell formation with studies from nucleoside transporter-deficient mice providing additional insights into the regulation of mammalian hematopoiesis. Furthermore, several idiopathic human genetic disorders have revealed nucleoside transport as an important component of mammalian hematopoiesis because mutations in individual nucleoside transporter genes are linked to various hematological abnormalities, including anemia. Here, we review recent developments in nucleoside transporters, including their transport characteristics, their role in the regulation of hematopoiesis, and their potential involvement in the occurrence of adverse hematological side effects due to nucleoside drug treatment. Furthermore, we discuss the putative mechanisms by which aberrant nucleoside transport may contribute to hematological abnormalities and identify the knowledge gaps where future research may positively impact treatment outcomes for patients undergoing various nucleoside analog therapies.
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Affiliation(s)
- Syed Saqib Ali
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Ruchika Raj
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Tejinder Kaur
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Brenna Weadick
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Debasis Nayak
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Minnsung No
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Jane Protos
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Hannah Odom
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Kajal Desai
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Avinash K. Persaud
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
| | - Joanne Wang
- Department of Pharmaceutics, College of Pharmacy, University of Washington, Seattle, WA 98195, USA;
| | - Rajgopal Govindarajan
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA; (S.S.A.); (R.R.); (T.K.); (B.W.); (D.N.); (M.N.); (J.P.); (H.O.); (K.D.); (A.K.P.)
- Translational Therapeutics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +1-614-247-8269; Fax: +1-614-292-2588
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20
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Leick MB, Silva H, Scarfò I, Larson R, Choi BD, Bouffard AA, Gallagher K, Schmidts A, Bailey SR, Kann MC, Jan M, Wehrli M, Grauwet K, Horick N, Frigault MJ, Maus MV. Non-cleavable hinge enhances avidity and expansion of CAR-T cells for acute myeloid leukemia. Cancer Cell 2022; 40:494-508.e5. [PMID: 35452603 PMCID: PMC9107929 DOI: 10.1016/j.ccell.2022.04.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/09/2021] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy is effective in lymphoid malignancies, but there has been limited data in myeloid cancers. Here, we start with a CD27-based CAR to target CD70 ("native") in acute myeloid leukemia (AML), and we find modest efficacy in vivo, consistent with prior reports. We then use orthogonal approaches to increase binding on both the tumor and CAR-T cell sides of the immune synapse: a pharmacologic approach (azacitidine) to increase antigen density of CD70 in myeloid tumors, and an engineering approach to stabilize binding of the CAR to CD70. To accomplish the latter, we design a panel of hinge-modified regions to mitigate cleavage of the extracellular portion of CD27. Our CD8 hinge and transmembrane-modified CD70 CAR-T cells are less prone to cleavage, have enhanced binding avidity, and increased expansion, leading to more potent in vivo activity. This enhanced CD70-targeted CAR is a promising candidate for further clinical development.
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Affiliation(s)
- Mark B Leick
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Blood and Marrow Transplant Program, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Harrison Silva
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Irene Scarfò
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca Larson
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Bryan D Choi
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Amanda A Bouffard
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Kathleen Gallagher
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Andrea Schmidts
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Stefanie R Bailey
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Michael C Kann
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Max Jan
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marc Wehrli
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Korneel Grauwet
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Nora Horick
- Department of Biostatistics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Matthew J Frigault
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Blood and Marrow Transplant Program, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marcela V Maus
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Blood and Marrow Transplant Program, Massachusetts General Hospital, Boston, MA 02114, USA.
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21
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Byrnes JR, Weeks AM, Shifrut E, Carnevale J, Kirkemo L, Ashworth A, Marson A, Wells JA. Hypoxia Is a Dominant Remodeler of the Effector T Cell Surface Proteome Relative to Activation and Regulatory T Cell Suppression. Mol Cell Proteomics 2022; 21:100217. [PMID: 35217172 PMCID: PMC9006863 DOI: 10.1016/j.mcpro.2022.100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 01/02/2023] Open
Abstract
Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the antitumor immune response. T cell surface receptors and surface proteins that influence interactions and function in the TME are proven targets for cancer immunotherapy. However, how the entire surface proteome remodels in primary human T cells in response to specific suppressive factors in the TME remains to be broadly and systematically characterized. Here, using a reductionist cell culture approach with primary human T cells and stable isotopic labeling with amino acids in cell culture-based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8+ surface proteome (surfaceome). Surprisingly, coculturing primary CD8+ T cells with Tregs only modestly affected the CD8+ surfaceome but did partially reverse activation-induced surfaceomic changes. In contrast, hypoxia drastically altered the CD8+ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4+ T cell surfaceome similarly responded to hypoxia, revealing a common hypoxia-induced surface receptor program. Our surfaceomics findings suggest that hypoxic environments create a challenge for T cell activation. These studies provide global insight into how Tregs and hypoxia remodel the T cell surfaceome and we believe represent a valuable resource to inform future therapeutic efforts to enhance T cell function.
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Affiliation(s)
- James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Amy M Weeks
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA; Gladstone Institutes, San Francisco, California, USA
| | - Julia Carnevale
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Lisa Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Alan Ashworth
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA; The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA; Gladstone Institutes, San Francisco, California, USA; Department of Medicine, University of California, San Francisco, San Francisco, California, USA; The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA; Parker Institute for Cancer Immunotherapy, San Francisco, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA.
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22
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Yang C, Zhang Q, Tang X, Wang B, Guan M, Tang G, Wu Z. BRCA2 promoter hypermethylation as a biomarker for the leukemic transformation of myeloproliferative neoplasms. Epigenomics 2022; 14:391-403. [PMID: 35259923 DOI: 10.2217/epi-2022-0025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To characterize the actionable biomarker for leukemic transformation (LT) of myeloproliferative neoplasms (MPNs) at the DNA damage repair promoter methylation level. Materials & methods: Bioinformatic analysis and experimental validation were performed to identify the MPNs-LT specific biomarker out of the promoter methylation of 236 DNA damage repair genes with GSE42042 dataset and an in-house cohort of 80 MPNs. Results: Hypermethylation of BRCA2 promoter was characterized as the JAK2 mutation-independent epigenetic marker for MPNs-LT and repressed mRNA and protein expression, leading to olaparib hypersensitivity in the leukemic cells from MPNs-LT. Conclusion: Expressional silence of BRCA2 by promoter methylation compels the homologous recombination deficiency and vulnerability to PARP inhibition and serves as an actionable marker for targeted therapy for MPNs-LT.
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Affiliation(s)
- Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Qingyun Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Binbin Wang
- Department of Hematology Laboratory Center, Changhai Hospital, Navy Military Medical University, Shanghai, 200433, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.,Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Gusheng Tang
- Department of Hematology Laboratory Center, Changhai Hospital, Navy Military Medical University, Shanghai, 200433, China
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.,Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
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23
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Pharmacological Modulation and (Patho)Physiological Roles of TRPM4 Channel-Part 2: TRPM4 in Health and Disease. Pharmaceuticals (Basel) 2021; 15:ph15010040. [PMID: 35056097 PMCID: PMC8779181 DOI: 10.3390/ph15010040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 02/06/2023] Open
Abstract
Transient receptor potential melastatin 4 (TRPM4) is a unique member of the TRPM protein family and, similarly to TRPM5, is Ca2+ sensitive and permeable for monovalent but not divalent cations. It is widely expressed in many organs and is involved in several functions; it regulates membrane potential and Ca2+ homeostasis in both excitable and non-excitable cells. This part of the review discusses the currently available knowledge about the physiological and pathophysiological roles of TRPM4 in various tissues. These include the physiological functions of TRPM4 in the cells of the Langerhans islets of the pancreas, in various immune functions, in the regulation of vascular tone, in respiratory and other neuronal activities, in chemosensation, and in renal and cardiac physiology. TRPM4 contributes to pathological conditions such as overactive bladder, endothelial dysfunction, various types of malignant diseases and central nervous system conditions including stroke and injuries as well as in cardiac conditions such as arrhythmias, hypertrophy, and ischemia-reperfusion injuries. TRPM4 claims more and more attention and is likely to be the topic of research in the future.
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24
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Zaib S, Rana N, Khan I. Histone modifications and their role in epigenetics of cancer. Curr Med Chem 2021; 29:2399-2411. [PMID: 34749606 DOI: 10.2174/0929867328666211108105214] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic regulations play a crucial role in the expression of various genes that are important in the normal cell function. Any alteration in these epigenetic mechanisms can lead to the modification of histone and DNA resulting in the silencing or enhanced expression of some genes causing various diseases. Acetylation, methylation, ribosylation or phosphorylation of histone proteins modifies its interaction with the DNA, consequently changing the ratio of heterochromatin and euchromatin. Terminal lysine residues of histone proteins serve as potential targets of such epigenetic modifications. The current review focuses on the histone modifications, their contributing factors, role of these modifications on metabolism leading to cancer and methylation of histone in cancer affects the DNA repair mechanisms.
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Affiliation(s)
- Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore-54590. Pakistan
| | - Nehal Rana
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore-54590. Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN. United Kingdom
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25
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Garcia-Manero G, Döhner H, Wei AH, La Torre I, Skikne B, Beach CL, Santini V. Oral Azacitidine (CC-486) for the Treatment of Myeloid Malignancies. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2021; 22:236-250. [PMID: 34758945 DOI: 10.1016/j.clml.2021.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023]
Abstract
Epigenetic dysregulation leads to aberrant DNA hypermethylation and is common in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). A large number of clinical trials in AML, MDS, and other hematologic malignancies have assessed hypomethylating agents (HMAs), used alone or in combination with other drugs, in the frontline, maintenance, relapsed/refractory, and peritransplant settings. Effective maintenance therapy has long been a goal for patients with AML in remission. Previous large, randomized clinical trials of maintenance with HMAs or other agents had not shown meaningful improvement in overall survival. Oral azacitidine (Oral-AZA [CC-486]) is approved in the United States, Canada, and European Union for treatment of adult patients with AML in first complete remission (CR) or CR with incomplete blood count recovery (CRi) following intensive induction chemotherapy who are ineligible for hematopoietic cell transplant. Regulatory approvals of Oral-AZA were based on outcomes from the randomized, phase III QUAZAR AML-001 trial, which showed a median overall survival advantage of 9.9 months with Oral-AZA versus placebo. Oral-AZA allows convenient extended AZA dosing for 14 days per 28-day treatment cycle, which is not feasible with injectable AZA. Focusing on AML and MDS, this report reviews the rationale for the use of orally bioavailable AZA and its potential use in all-oral combination therapy regimens; the unique pharmacokinetic and pharmacodynamic profile of Oral-AZA compared with injectable AZA; the clinical safety and efficacy of Oral-AZA maintenance therapy in patients with AML in first remission and for treatment of patients with active MDS; and ongoing Oral-AZA clinical trials.
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Affiliation(s)
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Andrew H Wei
- Department of Clinical Haematology, The Alfred Hospital, Melbourne, Australia; Monash University, Australian Centre for Blood Diseases, Melbourne, Australia
| | | | - Barry Skikne
- Bristol-Myers Squibb Company, Princeton, NJ; Department of Hematology, University of Kansas Medical Center, Kansas City, KS
| | - C L Beach
- Bristol-Myers Squibb Company, Princeton, NJ
| | - Valeria Santini
- MDS Unit, Hematology, AOU Careggi, University of Florence, Florence, Italy
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26
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Li Y, Feng Y, Si X, Zhao C, Wang F, Niu X. Genetic Expression Screening of Arsenic Trioxide-Induced Cytotoxicity in KG-1a Cells Based on Bioinformatics Technology. Front Genet 2021; 12:654826. [PMID: 34413873 PMCID: PMC8369888 DOI: 10.3389/fgene.2021.654826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022] Open
Abstract
Acute myeloid leukemia (AML) is a malignant tumor of the hematopoietic system, and leukemia stem cells are responsible for AML chemoresistance and relapse. KG-1a cell is considered a leukemia stem cell-enriched cell line, which is resistant to chemotherapy. Arsenic trioxide (ATO) is effective against acute promyelocytic leukemia as a first-line treatment agent, even as remission induction of relapsed cases. ATO has a cytotoxic effect on KG-1a cells, but the mechanism remains unclear. Our results demonstrated that ATO can inhibit cell proliferation, induce apoptosis, and arrest KG-1a cells in the G2/M phase. Using transcriptome analysis, we investigated the candidate target genes regulated by ATO in KG-1a cells. The expression profile analysis showed that the ATO had significantly changed gene expression related to proliferation, apoptosis, and cell cycle. Moreover, MYC, PCNA, and MCM7 were identified as crucial hub genes through protein-protein interaction network analysis; meanwhile, the expressions of them in both RNA and protein levels are down-regulated as confirmed by quantitative polymerase chain reaction and Western blot. Thus, our study suggests that ATO not only inhibits the expression of MYC, PCNA, and MCM7 but also leads to cell cycle arrest and apoptosis in KG-1a cells. Overall, this study provided reliable clues for improving the ATO efficacy in AML.
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Affiliation(s)
- Yahui Li
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Yingjie Feng
- The Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaohui Si
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Chenjin Zhao
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Fanping Wang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Xinqing Niu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
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27
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Ureshino H, Kurahashi Y, Watanabe T, Yamashita S, Kamachi K, Yamamoto Y, Fukuda-Kurahashi Y, Yoshida-Sakai N, Hattori N, Hayashi Y, Kawaguchi A, Tohyama K, Okada S, Harada H, Ushijima T, Kimura S. Silylation of Deoxynucleotide Analog Yields an Orally Available Drug with Antileukemia Effects. Mol Cancer Ther 2021; 20:1412-1421. [PMID: 34045225 PMCID: PMC9398096 DOI: 10.1158/1535-7163.mct-20-1125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
DNA methyltransferase inhibitors have improved the prognosis of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). However, because these agents are easily degraded by cytidine deaminase (CDA), they must be administered intravenously or subcutaneously. Recently, two orally bioavailable DNA methyltransferase inhibitors, CC-486 and ASTX727, were approved. In previous work, we developed 5-O-trialkylsilylated decitabines that resist degradation by CDA. However, the effects of silylation of a deoxynucleotide analog and enzymatic cleavage of silylation have not been fully elucidated. Enteric administration of OR21 in a cynomolgus monkey model led to high plasma concentrations and hypomethylation, and in a mouse model, oral administration of enteric-coated OR21 led to high plasma concentrations. The drug became biologically active after release of decitabine (DAC) from OR21 following removal of the 5'-O-trisilylate substituent. Toxicities were tolerable and lower than those of DAC. Transcriptome and methylome analysis of MDS and AML cell lines revealed that OR21 increased expression of genes associated with tumor suppression, cell differentiation, and immune system processes by altering regional promoter methylation, indicating that these pathways play pivotal roles in the action of hypomethylating agents. OR21 induced cell differentiation via upregulation of the late cell differentiation drivers CEBPE and GATA-1 Thus, silylation of a deoxynucleotide analog can confer oral bioavailability without new toxicities. Both in vivo and in vitro, OR21 exerted antileukemia effects, and had a better safety profile than DAC. Together, our findings indicate that OR21 is a promising candidate drug for phase I study as an alternative to azacitidine or decitabine.
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Affiliation(s)
- Hiroshi Ureshino
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Tatsuro Watanabe
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuharu Kamachi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuta Yamamoto
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Fukuda-Kurahashi
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan
| | - Nao Yoshida-Sakai
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshihiro Hayashi
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Kaoru Tohyama
- Department of Laboratory Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto, Japan
| | - Hironori Harada
- Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinya Kimura
- Department of Drug Discovery and Biomedical Sciences, Faculty of Medicine, Saga University, Saga, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Corresponding Author: Shinya Kimura, Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga University School of Medicine, 5-1-1 Nabeshima, Saga 849-8501, Japan. Phone: 81-952-34-2366; Fax: 81-952-34-2017; E-mail:
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28
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Dembitz V, Gallipoli P. The Role of Metabolism in the Development of Personalized Therapies in Acute Myeloid Leukemia. Front Oncol 2021; 11:665291. [PMID: 34094959 PMCID: PMC8170311 DOI: 10.3389/fonc.2021.665291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/26/2021] [Indexed: 01/17/2023] Open
Abstract
Despite significant recent advances in our understanding of the biology and genetics of acute myeloid leukemia (AML), current AML therapies are mostly based on a backbone of standard chemotherapy which has remained mostly unchanged for over 20 years. Several novel therapies, mostly targeting neomorphic/activating recurrent mutations found in AML patients, have only recently been approved following encouraging results, thus providing the first evidence of a more precise and personalized approach to AML therapy. Rewired metabolism has been described as a hallmark of cancer and substantial evidence of its role in AML establishment and maintenance has been recently accrued in preclinical models. Interestingly, unique metabolic changes are generated by specific AML recurrent mutations or in response to diverse AML therapies, thus creating actionable metabolic vulnerabilities in specific patient groups. In this review we will discuss the current evidence supporting a role for rewired metabolism in AML pathogenesis and how these metabolic changes can be leveraged to develop novel personalized therapies.
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Affiliation(s)
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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29
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Kordella C, Lamprianidou E, Kotsianidis I. Mechanisms of Action of Hypomethylating Agents: Endogenous Retroelements at the Epicenter. Front Oncol 2021; 11:650473. [PMID: 33768008 PMCID: PMC7985079 DOI: 10.3389/fonc.2021.650473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/04/2021] [Indexed: 12/28/2022] Open
Abstract
Abnormal DNA methylation patterns are thought to drive the pathobiology of high-risk myelodysplastic syndromes (HR-MDS) and acute myeloid leukemia (AML). Sixteen years after their initial approval, the hypomethylating agents (HMAs), 5-azacytidine (AZA) and 5-aza-2′-deoxycytidine, remain the mainstay of treatment for HR-MDS and AML. However, a connection of the hypomethylating or additional effects of HMAs with clinical responses remains yet to be shown, and the mode of action of HMAs remains obscure. Given the relatively short-lived responses and the inevitable development of resistance in HMAs, a thorough understanding of the antineoplastic mechanisms employed by HMAs holds critical importance. Recent data in cancer cell lines demonstrate that reactivation of endogenous retroelements (EREs) and induction of a cell-intrinsic antiviral response triggered by RNA neotranscripts may underlie the antitumor activity of HMAs. However, data on primary CD34+ cells derived from patients with HR-MDS failed to confirm a link between HMA-mediated ERE modulation and clinical response. Though difficult to reconcile the apparent discrepancy, it is possible that HMAs mediate their effects in more advanced levels of differentiation where cells become responsive to interferon, whereas, inter-individual variations in the process of RNA editing and, in particular, in the ADAR1/OAS/RNase L pathway may also confound the associations of clinical response with the induction of viral mimicry. Further ex vivo studies along with clinical correlations in well-annotated patient cohorts are warranted to decipher the role of ERE derepression in the antineoplastic mechanisms of HMAs.
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Affiliation(s)
- Chryssoula Kordella
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eleftheria Lamprianidou
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
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30
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Li Y, Wang Y, Yao Y, Lyu J, Qiao Q, Mao J, Xu Z, Ye M. Rapid Enzyme-Mediated Biotinylation for Cell Surface Proteome Profiling. Anal Chem 2021; 93:4542-4551. [PMID: 33660993 DOI: 10.1021/acs.analchem.0c04970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell surface is the primary site for sensing extracellular stimuli. The knowledge of the transient changes on the surfaceome upon a perturbation is very important as the initial changed proteins could be driving molecules for some phenotype. In this study, we report a fast cell surface labeling strategy based on peroxidase-mediated oxidative tyrosine coupling strategy, enabling efficient and selective cell surface labeling within seconds. With a labeling time of 1 min, 2684 proteins, including 1370 (51%) cell surface-annotated proteins (cell surface/plasma membrane/extracellular), 732 transmembrane proteins, and 81 cluster of differentiation antigens, were identified from HeLa cells. By comparison with the negative control experiment using quantitative proteomics, 500 (68%) out of the 731 significantly enriched proteins (p-value < 0.05, ≥2-fold) in positive experimental samples were cell surface-annotated proteins. Finally, this technology was applied to track the dynamic changes of the surfaceome upon insulin stimulation at two time points (5 min and 2 h) in HepG2 cells. Thirty-two proteins, including INSR, CTNNB1, TFRC, IGF2R, and SORT1, were found to be significantly regulated (p-value < 0.01, ≥1.5-fold) after insulin exposure by different mechanisms. We envision that this technique could be a powerful tool to analyze the transient changes of the surfaceome with a good time resolution and to delineate the temporal and spatial regulation of cellular signaling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yating Yao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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31
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Chen W, Mou KY, Solomon P, Aggarwal R, Leung KK, Wells JA. Large remodeling of the Myc-induced cell surface proteome in B cells and prostate cells creates new opportunities for immunotherapy. Proc Natl Acad Sci U S A 2021; 118:e2018861118. [PMID: 33483421 PMCID: PMC7848737 DOI: 10.1073/pnas.2018861118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
MYC is a powerful transcription factor overexpressed in many human cancers including B cell and prostate cancers. Antibody therapeutics are exciting opportunities to attack cancers but require knowledge of surface proteins that change due to oncogene expression. To identify how MYC overexpression remodels the cell surface proteome in a cell autologous fashion and in different cell types, we investigated the impact of MYC overexpression on 800 surface proteins in three isogenic model cell lines either of B cell or prostate cell origin engineered to have high or low MYC levels. We found that MYC overexpression resulted in dramatic remodeling (both up- and down-regulation) of the cell surfaceome in a cell type-dependent fashion. We found systematic and large increases in distinct sets of >80 transporters including nucleoside transporters and nutrient transporters making cells more sensitive to toxic nucleoside analogs like cytarabine, commonly used for treating hematological cancers. Paradoxically, MYC overexpression also increased expression of surface proteins driving cell turnover such as TNFRSF10B, also known as death receptor 5, and immune cell attacking signals such as the natural killer cell activating ligand NCR3LG1, also known as B7-H6. We generated recombinant antibodies to these two targets and verified their up-regulation in MYC overexpression cell lines and showed they were sensitive to bispecific T cell engagers (BiTEs). Our studies demonstrate how MYC overexpression leads to dramatic bidirectional remodeling of the surfaceome in a cell type-dependent but functionally convergent fashion and identify surface targets or combinations thereof as possible candidates for cytotoxic metabolite or immunotherapy.
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Affiliation(s)
- Wentao Chen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Department of Therapeutic Discovery, Amgen Research, Thousand Oaks, CA 91320
| | - Kurt Yun Mou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 11529
| | - Paige Solomon
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Rahul Aggarwal
- Department of Medicine, University of California, San Francisco, CA 94158
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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32
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Takam Kamga P, Bazzoni R, Dal Collo G, Cassaro A, Tanasi I, Russignan A, Tecchio C, Krampera M. The Role of Notch and Wnt Signaling in MSC Communication in Normal and Leukemic Bone Marrow Niche. Front Cell Dev Biol 2021; 8:599276. [PMID: 33490067 PMCID: PMC7820188 DOI: 10.3389/fcell.2020.599276] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Notch and Wnt signaling are highly conserved intercellular communication pathways involved in developmental processes, such as hematopoiesis. Even though data from literature support a role for these two pathways in both physiological hematopoiesis and leukemia, there are still many controversies concerning the nature of their contribution. Early studies, strengthened by findings from T-cell acute lymphoblastic leukemia (T-ALL), have focused their investigation on the mutations in genes encoding for components of the pathways, with limited results except for B-cell chronic lymphocytic leukemia (CLL); in because in other leukemia the two pathways could be hyper-expressed without genetic abnormalities. As normal and malignant hematopoiesis require close and complex interactions between hematopoietic cells and specialized bone marrow (BM) niche cells, recent studies have focused on the role of Notch and Wnt signaling in the context of normal crosstalk between hematopoietic/leukemia cells and stromal components. Amongst the latter, mesenchymal stromal/stem cells (MSCs) play a pivotal role as multipotent non-hematopoietic cells capable of giving rise to most of the BM niche stromal cells, including fibroblasts, adipocytes, and osteocytes. Indeed, MSCs express and secrete a broad pattern of bioactive molecules, including Notch and Wnt molecules, that support all the phases of the hematopoiesis, including self-renewal, proliferation and differentiation. Herein, we provide an overview on recent advances on the contribution of MSC-derived Notch and Wnt signaling to hematopoiesis and leukemia development.
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Affiliation(s)
- Paul Takam Kamga
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
- EA4340-BCOH, Biomarker in Cancerology and Onco-Haematology, UVSQ, Université Paris Saclay, Boulogne-Billancourt, France
| | - Riccardo Bazzoni
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Giada Dal Collo
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adriana Cassaro
- Hematology Unit, Department of Oncology, Niguarda Hospital, Milan, Italy
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Ilaria Tanasi
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Anna Russignan
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Cristina Tecchio
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Mauro Krampera
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
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33
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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34
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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35
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Hernandes LC, Machado ART, Tuttis K, Ribeiro DL, Aissa AF, Dévoz PP, Antunes LMG. Caffeic acid and chlorogenic acid cytotoxicity, genotoxicity and impact on global DNA methylation in human leukemic cell lines. Genet Mol Biol 2020; 43:e20190347. [PMID: 32644097 PMCID: PMC7350414 DOI: 10.1590/1678-4685-gmb-2019-0347] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Dietary phenolic compounds such as caffeic and chlorogenic acid exert an antiproliferative effect and modulate the gene-specific DNA methylation status in human breast tumor cells, but it remains unclear whether they interfere with global DNA methylation in human leukemia cells. We examined whether caffeic and chlorogenic acid (1-250 µM) exert antitumor action in human promyelocytic leukemia cells (HL-60) and human acute T-cell leukemia cells (Jurkat). Caffeic and chlorogenic acid did not reduce cell viability in the two cell lines, as assessed using the neutral red uptake and MTT assays. These phenolic acids (1-100 μM) neither induced DNA damage (comet assay) nor increased the micronuclei frequency (micronucleus assay) in HL-60 and Jurkat cells, indicating that they were not genotoxic or mutagenic. Analysis of global DNA methylation levels using a 5-mC DNA ELISA kit revealed that chlorogenic acid at a non-cytotoxic concentration (100 μM) induced global DNA hypomethylation in Jurkat cells, but not in HL-60 cells, suggesting that it exerts a cell-specific effect. Caffeic acid did not change global DNA methylation. As other phenolic compounds, chlorogenic acid probably modulates DNA methylation by targeting DNA methyltransferases. The hypomethylating action of chlorogenic acid can be beneficial against hematological malignances whose pathogenic processes involve impairment of DNA methylation.
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Affiliation(s)
- Lívia Cristina Hernandes
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Ribeirão Preto, SP, Brazil
| | - Ana Rita Thomazela Machado
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Ribeirão Preto, SP, Brazil
| | - Katiuska Tuttis
- Universidade de São Paulo USP, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Diego Luís Ribeiro
- Universidade de São Paulo USP, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Alexandre Ferro Aissa
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Ribeirão Preto, SP, Brazil
| | - Paula Pícoli Dévoz
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Ribeirão Preto, SP, Brazil
| | - Lusânia Maria Greggi Antunes
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Ribeirão Preto, SP, Brazil
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Aberrant TRPM4 expression in MLL-rearranged acute myeloid leukemia and its blockade induces cell cycle arrest via AKT/GLI1/Cyclin D1 pathway. Cell Signal 2020; 72:109643. [PMID: 32320859 DOI: 10.1016/j.cellsig.2020.109643] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/24/2020] [Accepted: 04/15/2020] [Indexed: 02/05/2023]
Abstract
Transient Receptor Potential Melastatin Subfamily Member 4 (TRPM4) has been demonstrated to be aberrantly expressed in several cancers but seldom reported in acute leukemia. Based on database mining and validated experiments, our present data show that TRPM4 is selectively overexpressed in AML patients and cell lines with the MLL gene rearrangement. We analyzed the correlation between TRPM4 expression and clinical parameters in a validated cohort of AML patients. Increased TRPM4 expression was associated with significant leukocytosis (p = .028), M4/M5 subtype (p = .000), FLT3-ITD mutation (p = .034), MLL status (p = .007) and a higher risk stratification (p = .001). Knockdown of TRPM4 mediated by siRNA impaired proliferation and arrested the cell cycle at the G0/G1 phase in MLL-rearranged leukemia cells. We suggested that TRPM4 may be involved in the pathogenesis of MLL-rearranged leukemia through regulating the AKT/GLI1/Cyclin D1 pathway. The transcription factor HOXA9 was found to be responsible for upregulation of TRPM4 expression by binding to its promoter. In conclusion, TRPM4 is overexpressed in MLL-rearranged AML and blockade of TRPM4 may be an alternative therapeutic approach in AML patients with high TRPM4 expression.
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Leung KK, Wilson GM, Kirkemo LL, Riley NM, Coon JJ, Wells JA. Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proc Natl Acad Sci U S A 2020; 117:7764-7775. [PMID: 32205440 PMCID: PMC7148585 DOI: 10.1073/pnas.1917947117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK, and AKT. We find that each oncogene has somewhat different surfaceomes, but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome and differential increases in complex hybrid glycans, especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems-level view of how specific driver oncogenes remodel the surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.
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Affiliation(s)
- Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143;
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Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
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Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
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Passet M, Lepelletier C, Vignon-Pennamen MD, Chasset F, Hirsch P, Battistella M, Duriez P, Sicre de Fontbrune F, Boissel N, Legrand O, Raffoux E, Bagot M, Adès L, Clappier E, Bouaziz JD. Next-Generation Sequencing in Myeloid Neoplasm-Associated Sweet's Syndrome Demonstrates Clonal Relation between Malignant Cells and Skin-Infiltrating Neutrophils. J Invest Dermatol 2020; 140:1873-1876.e5. [PMID: 32081610 DOI: 10.1016/j.jid.2019.12.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/27/2019] [Accepted: 12/14/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Marie Passet
- Hematology Laboratory, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U944/CNRS UMR7212, Institut de Recherche Saint-Louis, Paris, France; Université de Paris, Paris, France
| | - Clémence Lepelletier
- Université de Paris, Paris, France; INSERM UMR976, Centre de Recherche sur la Peau, Paris, France; Dermatology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - François Chasset
- Dermatology Department, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Pierre Hirsch
- Hematology Laboratory, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France; Sorbonne Université, INSERM U938, Centre de Recherche Saint-Antoine (CRSA), F-75012 Paris, France
| | - Maxime Battistella
- Université de Paris, Paris, France; INSERM UMR976, Centre de Recherche sur la Peau, Paris, France; Pathology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Paul Duriez
- Pathology Department, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Flore Sicre de Fontbrune
- Bone Marrow Transplant Unit, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Boissel
- Université de Paris, Paris, France; Hematology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Ollivier Legrand
- Sorbonne Université, INSERM U938, Centre de Recherche Saint-Antoine (CRSA), F-75012 Paris, France; Hematology Department, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Raffoux
- Hematology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Martine Bagot
- Université de Paris, Paris, France; INSERM UMR976, Centre de Recherche sur la Peau, Paris, France; Dermatology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lionel Adès
- INSERM U944/CNRS UMR7212, Institut de Recherche Saint-Louis, Paris, France; Université de Paris, Paris, France; Bone Marrow Transplant Unit, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuelle Clappier
- Hematology Laboratory, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U944/CNRS UMR7212, Institut de Recherche Saint-Louis, Paris, France; Université de Paris, Paris, France
| | - Jean-David Bouaziz
- Université de Paris, Paris, France; INSERM UMR976, Centre de Recherche sur la Peau, Paris, France; Dermatology Department, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.
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40
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Liu XL, Liu HQ, Li J, Mao CY, He JT, Zhao X. Role of epigenetic in leukemia: From mechanism to therapy. Chem Biol Interact 2020; 317:108963. [PMID: 31978391 DOI: 10.1016/j.cbi.2020.108963] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/09/2020] [Accepted: 01/20/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic variations can play remarkable roles in different normal and abnormal situations. Such variations have been shown to have a direct role in the pathogenesis of various diseases either through inhibition of tumor suppressor genes or increasing the expression of oncogenes. Enzymes involving in epigenetic machinery are the main actors in tuning the epigenetic-based controls on gene expressions. Aberrant expression of these enzymes can trigger big chaos in the cellular gene expression networks and finally lead to cancer progression. This situation has been shown in different types of leukemia, where high or low levels of an epigenetic enzyme are partly or highly responsible for the involvement or progression of a disease. DNA hypermethylation, different histone modifications, and aberrant miRNA expressions are three main epigenetic variations, which have been shown to play a role in leukemia progression. Epigenetic based treatments now are considered as novel and effective therapies in order to decrease the abnormal epigenetic modifications in patient cells. Different epigenetic-based approaches have been developed and tested to inhibit or reverse the unusual expression of epigenetic agents in leukemia. Acute myeloid leukemia (AML), the most prevalent acute leukemia in adults, is anaggressive hematological malignancy arising in hematopoietic stem and progenitor cells. With the exception of a few specific AML subtypes, the mainstays of treatment have not significantly changed over the last 20 years, and are still based on standard cytotoxic chemotherapy. In this review, we will discuss the recent development of therapeutics specifically targeting these key epigenetic programs in AML, describe their mechanism of action and present their current clinical development. Finally, we will discuss the opportunities presented by epigenetically targeted therapy in AML and will highlight future challenges ahead for the AML community, to ensure that this novel therapeutics are optimally translated into clinical practice and result in clinical improvement for AML patients.
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Affiliation(s)
- Xiao-Liang Liu
- Department of Hematology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Huan-Qiu Liu
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Ji Li
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Cui-Ying Mao
- Department of Cardiology, China-Japan Union Hospital, Jilin University, Changchun, 130033, Jilin Province, China
| | - Jin-Ting He
- Department of Neurology, China-Japan Union Hospital, Jilin University, Changchun, 130033, Jilin Province, China.
| | - Xin Zhao
- Department of Paediatrics, The First Hospital of Jilin University, Changchun, Jilin, 130021, China.
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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42
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Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
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43
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Sun F, Wu R. Systematic and site-specific analysis of N-glycoproteins on the cell surface by integrating bioorthogonal chemistry and MS-based proteomics. Methods Enzymol 2019; 626:223-247. [PMID: 31606076 DOI: 10.1016/bs.mie.2019.06.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glycoproteins on the cell surface are essential for various cellular activities including cell-cell communication and cell-matrix interaction. Alterations of glycosylation are correlated with many diseases such as cancer and infectious diseases. However, it is greatly challenging to systematically and site-specially analyze glycoproteins only located on cell surface because of the heterogeneity of glycans, the low abundance of many surface glycoproteins and the requirement of effective methods to separate surface glycoproteins. In this chapter, we briefly review existing mass spectrometry (MS)-based methods for global analysis of surface glycoproteins. Then we discuss an effective method integrating metabolic labeling, click and enzymatic reactions, and MS-based proteomics to comprehensively and site-specifically investigate cell surface N-glycoproteins. A detailed protocol for this method is also included. In combination with quantitative proteomics, we applied this method to quantify cell surface N-glycoproteins and study the relationship between cell invasiveness and N-sialoglycoproteins on the cell surface. Considering the importance of surface glycoproteins, this method can be extensively applied to advance glycoscience, which leads to a better understanding of the molecular mechanisms of human diseases, and the discovery of surface glycoproteins as biomarkers for disease detection.
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, United States.
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44
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Lamprianidou E, Zoulia E, Bernard E, Kordella C, Papoutselis M, Bezirgiannidou Z, Vrachiolias G, Papaemmanuil E, Kotsianidis I. Multifaceted modes of action of azacytidine: a riddle wrapped up in an enigma. Leuk Lymphoma 2019; 60:3277-3281. [PMID: 31185765 DOI: 10.1080/10428194.2019.1627542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Eleftheria Lamprianidou
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Emmanouela Zoulia
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Elsa Bernard
- Center for Molecular Oncology, Center for Heme Malignancies and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chryssoula Kordella
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Menelaos Papoutselis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Zoi Bezirgiannidou
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - George Vrachiolias
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
| | - Elli Papaemmanuil
- Center for Molecular Oncology, Center for Heme Malignancies and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ioannis Kotsianidis
- Department of Hematology, Democritus University of Thrace Medical School, Alexandroupolis, Greece
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